Log In
Sign Up
about
faq
Ask a question
Latest
News
Jobs
Tutorials
Tags
Users
New Post
Latest
News
Jobs
Tutorials
Tags
Users
Log In
Sign Up
About
Limit
all time
today
this week
this month
this year
Unanswered
All posts
Sort
Update
Answers
Bookmarks
Creation
Replies
Rank
Views
Votes
0
votes
0
replies
669
views
Error in serialization
scDblFinder
BiocParallel
17 months ago
Lluís Revilla Sancho
▴ 760
0
votes
1
reply
753
views
Retrieving Package Metadata from Bioconductor API: Versions and Dependencies
metaMSdata
updated 17 months ago by
shepherl
4.2k • written 17 months ago by
Sadman
• 0
4
votes
12
replies
5.9k
views
How to get DMR for Infinium methylation EPIC v2
ChAMP
DMRcate
minfi
updated 17 months ago by
Tim Peters
▴ 230 • written 2.1 years ago by
rae.alshammari
▴ 20
0
votes
3
replies
961
views
Trouble with creating Series RNA-seq normalized counts matrix
GEO
rnaseqGene
RNA
17 months ago
gallantk5
• 0
0
votes
3
replies
1.0k
views
Error when trying to do different pairwise comparisons and lfcshrink than what's listed on resultsNames()
RNASeqData
DESeq2
RNASeq
DifferentialExpression
updated 17 months ago by
ATpoint
★ 5.0k • written 17 months ago by
Mark
• 0
1
vote
1
reply
1.2k
views
Why does greyListChIP return different grey lists every time I newly run the script?
GreyListChIP
updated 17 months ago by
Matt Eldridge
▴ 10 • written 17 months ago by
Giulia
• 0
0
votes
0
replies
667
views
Using variantAnnotation to put together genotype and consequence information
variantAnn
VariantAnnotation
17 months ago
ramiro.barrantes
▴ 10
0
votes
8
replies
1.8k
views
Error running tximeta
tximeta
updated 16 months ago by
Guido Hooiveld
★ 4.1k • written 17 months ago by
daria.igudesman
• 0
0
votes
4
replies
1.5k
views
Generating surrogate variables across multiple variables of interest
sva
17 months ago • updated 16 months ago
Robert
• 0
1
vote
6
replies
1.3k
views
limma and Syntactically Invalid Factor Values
limma
updated 17 months ago by
Gordon Smyth
53k • written 17 months ago by
Dario Strbenac
★ 1.6k
1
vote
1
reply
1.1k
views
DEG Analysis using Limma on DSP GeoMx Data: Handling Multiple ROIs per Core
limma
DSP
GeomxTools
17 months ago
Bioinformagician
• 0
1
vote
3
replies
951
views
Doubt about model in paired samples (intercept ?)
DESeq2
updated 17 months ago by
Michael Love
43k • written 17 months ago by
picasa1983
• 0
0
votes
10
replies
2.1k
views
Two treatments, one control
DESeq2
stageR
17 months ago
alephreish
• 0
0
votes
2
replies
2.0k
views
How to correct for a covariate in DESeq2 that is linear with the condition of interest
DESeq2
17 months ago
Fiona
• 0
2
votes
3
replies
986
views
DeSeq2 Model Problems with species, tissue, and tissue status nesting
DESeq2
R
written 17 months ago by
tbiewerh
• 0
4
votes
2
replies
1.1k
views
Parallel comparison of two DNAString objects with IUPAC ambiguities
Biostrings
written 17 months ago by
maltethodberg
▴ 180
1
vote
1
reply
1.4k
views
Differences between core_enrichment from gsePathway and viewPathway
FunctionalAnalysis
clusterProfiler
viewPathway
gsePathway
updated 17 months ago by
Guido Hooiveld
★ 4.1k • written 17 months ago by
Filipe
• 0
0
votes
1
reply
697
views
methylKit problem
methylKit
updated 17 months ago by
alex.gos90
▴ 10 • written 17 months ago by
Krisztina
• 0
1
vote
3
replies
939
views
Create merged ChIP heatmap across conditions
DiffBind
profileplyr
updated 17 months ago by
Rory Stark
★ 5.2k • written 17 months ago by
jesswhitts
• 0
0
votes
0
replies
467
views
ASICS to process NMR spectra
ASICS
17 months ago
KONG ZHI XIAN
• 0
0
votes
0
replies
544
views
MAST package: Most appropriate way to perform lrTest for effect of factor with multiple levels in pairwise manner?
MAST
17 months ago
Kelly
• 0
5
votes
3
replies
1.1k
views
Limma comparing gene expression between base line and one treatment
limma
updated 17 months ago by
James W. MacDonald
68k • written 17 months ago by
AL
• 0
0
votes
1
reply
1.2k
views
How to rank DEG for GSEA using DEseq2 result ?
DESeq2
limma
GeneSetEnrichment
updated 17 months ago by
ATpoint
★ 5.0k • written 17 months ago by
picasa1983
• 0
0
votes
1
reply
567
views
Run DEXSeq successfully but got a result that padj==1 in all genes
DEXSeq
updated 17 months ago by
ATpoint
★ 5.0k • written 17 months ago by
2406691063
• 0
4
votes
9
replies
2.1k
views
Get_interactions is giving the combined score
STRINGdb
updated 17 months ago by
McKayl
• 0 • written 17 months ago by
nkavabhrath03
▴ 20
2
votes
5
replies
1.1k
views
Limma - 0 downreg and upreg values
GeoMx
limma
DifferentialExpression
updated 17 months ago by
James W. MacDonald
68k • written 17 months ago by
sop
• 0
4
votes
12
replies
1.9k
views
DGE with a Continuous Variable
DESeq2
model
updated 16 months ago by
Michael Love
43k • written 17 months ago by
picasa1983
• 0
0
votes
4
replies
892
views
Error from runShinyMethyl() - is(object, "shinyMethylSet") is not TRUE
shinyMethyl
updated 17 months ago by
James W. MacDonald
68k • written 17 months ago by
Courtney
• 0
1
vote
5
replies
3.2k
views
ComplexHeatmap - alter legend position
ComplexHeatmap
17 months ago
Lucy
▴ 60
4
votes
14
replies
2.7k
views
LIMMA 2x2 Factorial Design with Paired Samples
factorialdesign
limma
pairedsamples
updated 16 months ago by
Gordon Smyth
53k • written 17 months ago by
Michael E
• 0
0
votes
1
reply
700
views
T cell subtype annotation
SingleCellExperiment
updated 17 months ago by
James W. MacDonald
68k • written 17 months ago by
georgii.vdovin
• 0
0
votes
1
reply
768
views
minfi - bumphunter value problem
bumphunter
minfiData
minfi
bumphun
updated 17 months ago by
James W. MacDonald
68k • written 17 months ago by
kumakeren16
• 0
6
votes
7
replies
2.1k
views
findOverlaps(), queryHits and subjectHits()
GenomicFiles
updated 17 months ago by
Hervé Pagès
16k • written 17 months ago by
user_bioinfo
• 0
0
votes
0
replies
608
views
How to use GAGE with my own metagenomic KOFams data
kegg.gsets
gageData
gage
KEGG
17 months ago
cereyredondo
• 0
0
votes
1
reply
613
views
output from RAIN doesn't look rhythmic
rain
updated 17 months ago by
ATpoint
★ 5.0k • written 17 months ago by
cereyredondo
• 0
0
votes
3
replies
1.8k
views
Query regarding phyloseq object construct with QIIME output
phyloseq
microbiome
Metagenomics
updated 17 months ago by
Карина
• 0 • written 2.5 years ago by
abhisek001
• 0
1
vote
2
replies
767
views
DESeq2: two conditions two genotypes
DESeq2
17 months ago
Rocio
• 0
2
votes
4
replies
1.3k
views
DESeq normalized counts vs CQN and statistics
DESeq2
cqn
written 17 months ago by
emlucero
• 0
1
vote
4
replies
2.6k
views
Should I perform batch correction of normalized RNA-seq counts prior to GSVA?
GSVA
GSVAdata
RNAseq
17 months ago
Lucy
▴ 60
0
votes
2
replies
1.4k
views
Installing Bioconductor
Bioconductor
updated 17 months ago by
Lluís Revilla Sancho
▴ 760 • written 17 months ago by
mariyahgeorge14
• 0
0
votes
1
reply
606
views
featureCounts from Rsubread
Rsubread
updated 17 months ago by
Gordon Smyth
53k • written 17 months ago by
Emiliano
• 0
0
votes
0
replies
625
views
News:
EuroBioC2024 Carpentries workshops Sep 2-3
Community
Workshop
Bioconductor
EuroBioC2024
17 months ago
Maria Doyle
▴ 110
0
votes
1
reply
1.0k
views
Problem with spike-ins (ERCC) in DESeq2 analysis after doing RUVg!
SpikeIn
RUVSeq
DESeq2
RUV
updated 17 months ago by
Michael Love
43k • written 17 months ago by
Ειρήνη
• 0
5
votes
9
replies
2.9k
views
Inconsistent nullp and goseq enrichment results across operating systems
goseq
written 17 months ago by
Danielle
• 0
0
votes
4
replies
1.1k
views
DE analysis in EdgeR /Can any one please help me.
RNASeqData
DEGraph
RNASeq
edgeR
DegNorm
written 17 months ago by
Shaozhen
• 0
0
votes
4
replies
1.5k
views
Generating Gene Expression Levels from TSV files on GEO
GEOquery
GEO
TSV
updated 17 months ago by
Sean Davis
21k • written 17 months ago by
gallantk5
• 0
0
votes
0
replies
820
views
Linear Mixed Model for Differential Gene Expression in Single-Cell RNAseq with Batch Effects
lmer
MAST
DifferentialExpression
17 months ago
nhaus
▴ 70
3
votes
4
replies
1.3k
views
Differences in Limma and Dreamlet random effects from confounded dataset
limma
dreamlet
17 months ago
jcollier
• 0
0
votes
1
reply
949
views
ChAMP analysis Error: Meth Matrix and UnMeth Matrix seems not paried correctly AND incomplete final line
MethylationArray
methylationArrayAnalysis
ChAMP
updated 12 months ago by
nereaherrera23
• 0 • written 17 months ago by
Mathu
• 0
1
vote
0
replies
625
views
RUVg spike-in assumption global expression
RUVSeq
RUVnormalize
17 months ago
Erdi
▴ 10
46,696 results • Page
19 of 934
Recent ...
Replies
Answer: NUPOP usage
by
shepherl
4.2k
You should read the documentation in the package especially the package vignette https://bioconductor.org/packages/release/bioc/html/NuPoP.…
Comment: How can I correctly use phyloseq with Docker?
by
fnfgame
• 0
In a rocker image, this error usually means the Bioconductor install happened as root but the runtime library paths used by the shiny user …
Comment: DECIPHER DesignProbes unable to design FISH-probes
by
Erik Wright
▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment
by
Michael Love
43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment
by
Michael Love
43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Awards
• All
Popular Question
to
Dario Strbenac
★ 1.6k
Scholar
to
Nikos Ignatiadis
▴ 180
Popular Question
to
Robert
• 0
Popular Question
to
lamia11me
• 0
Popular Question
to
Gordon Smyth
53k
Locations
• All
USA,
29 minutes ago
The city by the bay,
47 minutes ago
United States,
2 hours ago
United States,
2 hours ago
United States,
3 hours ago
Traffic: 1326 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6